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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CTSB-FDFT1 (FusionGDB2 ID:20465)

Fusion Gene Summary for CTSB-FDFT1

check button Fusion gene summary
Fusion gene informationFusion gene name: CTSB-FDFT1
Fusion gene ID: 20465
HgeneTgene
Gene symbol

CTSB

FDFT1

Gene ID

1508

2222

Gene namecathepsin Bfarnesyl-diphosphate farnesyltransferase 1
SynonymsAPPS|CPSB|RECEUPDGPT|ERG9|SQS|SQSD|SS
Cytomap

8p23.1

8p23.1

Type of geneprotein-codingprotein-coding
Descriptioncathepsin BAPP secretaseamyloid precursor protein secretasecathepsin B1cysteine proteaseepididymis secretory sperm binding proteinsqualene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetase
Modification date2020031320200320
UniProtAcc

P07858

P37268

Ensembl transtripts involved in fusion geneENST00000415599, ENST00000345125, 
ENST00000353047, ENST00000434271, 
ENST00000453527, ENST00000530640, 
ENST00000531089, ENST00000533455, 
ENST00000534510, ENST00000525076, 
ENST00000220584, ENST00000538689, 
ENST00000443614, ENST00000446331, 
ENST00000525777, ENST00000525900, 
ENST00000528643, ENST00000528812, 
ENST00000530664, 
Fusion gene scores* DoF score24 X 19 X 10=456012 X 9 X 5=540
# samples 2511
** MAII scorelog2(25/4560*10)=-4.18903382439002
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/540*10)=-2.29545588352617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTSB [Title/Abstract] AND FDFT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTSB(11704560)-FDFT1(11695896), # samples:1
FDFT1(11667359)-CTSB(11701750), # samples:1
Anticipated loss of major functional domain due to fusion event.CTSB-FDFT1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CTSB-FDFT1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CTSB-FDFT1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCTSB

GO:0006508

proteolysis

7890620|8811434

HgeneCTSB

GO:0030574

collagen catabolic process

22952693

HgeneCTSB

GO:0051603

proteolysis involved in cellular protein catabolic process

22952693


check buttonFusion gene breakpoints across CTSB (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across FDFT1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4ESCATCGA-L5-A4OJCTSBchr8

11704560

-FDFT1chr8

11695896

+


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Fusion Gene ORF analysis for CTSB-FDFT1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000415599ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3CDSENST00000415599ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
3UTR-3UTRENST00000415599ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000345125ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000353047ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000434271ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000453527ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000530640ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000531089ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000533455ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
5CDS-3UTRENST00000534510ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000353047ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000353047ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000434271ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000434271ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000530640ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000530640ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000531089ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000531089ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000533455ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
Frame-shiftENST00000533455ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000345125ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000345125ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000453527ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000453527ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000534510ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
In-frameENST00000534510ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3CDSENST00000525076ENST00000220584CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3CDSENST00000525076ENST00000538689CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000443614CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000446331CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000525777CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000525900CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000528643CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000528812CTSBchr8

11704560

-FDFT1chr8

11695896

+
intron-3UTRENST00000525076ENST00000530664CTSBchr8

11704560

-FDFT1chr8

11695896

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CTSB-FDFT1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
CTSBchr811704560-FDFT1chr811695896+2.23E-050.9999777
CTSBchr811704560-FDFT1chr811695896+2.23E-050.9999777

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CTSB-FDFT1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:11704560/chr8:11695896)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CTSB

P07858

FDFT1

P37268

FUNCTION: Thiol protease which is believed to participate in intracellular degradation and turnover of proteins (PubMed:12220505). Cleaves matrix extracellular phosphoglycoprotein MEPE (PubMed:12220505). Involved in the solubilization of cross-linked TG/thyroglobulin in the thyroid follicle lumen (By similarity). Has also been implicated in tumor invasion and metastasis (PubMed:3972105). {ECO:0000250|UniProtKB:P10605, ECO:0000269|PubMed:12220505, ECO:0000269|PubMed:3972105}.FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269|PubMed:10896663, ECO:0000269|PubMed:24531458}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneFDFT1chr8:11704560chr8:11695896ENST0000022058468384_404344418.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneFDFT1chr8:11704560chr8:11695896ENST0000022058468284_304344418.0TransmembraneHelical


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Fusion Gene Sequence for CTSB-FDFT1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CTSB-FDFT1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CTSB-FDFT1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CTSB-FDFT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource